freebayes: freebayes.xml annotate

author	recetox
date	Fri, 14 Aug 2020 13:59:45 +0000
parents
children

rev	line source
0 13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	2 <description>bayesian genetic variant detector</description>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	3 <macros>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	4 <import>macros.xml</import>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	5 </macros>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	6 <expand macro="requirements">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	7 <requirement type="package" version="4.1.3">gawk</requirement>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	8 <requirement type="package" version="20170422">parallel</requirement>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	9 </expand>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	11 ##set up input files
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	12
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	13 #set $reference_fasta_filename = "localref.fa"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	14
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	15 #if str( $reference_source.reference_source_selector ) == "history":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	16 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	17 samtools faidx '${reference_fasta_filename}' 2>&1 \|\| echo "Error running samtools faidx for FreeBayes" >&2 &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	18 #else:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	20 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	21
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	22 #if $reference_source.batchmode.processmode == 'merge':
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	23 #set $input_bamfiles = $reference_source.batchmode.input_bams
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	24 #else:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	25 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	26 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	27
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	28 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	29 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	30 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	31 #end for
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	32
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	33 ## Tabixize optional input_variant_vcf file (for --variant-input option)
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	34 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	35 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	36 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	37 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	38
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	39 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	40 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	41 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	42 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	43 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	44 #else
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	45 ##divide up the regions in the bam file for efficient processing
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	46 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	47 samtools view -H b_${bam_count}.bam \|
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	48 grep '^@SQ' \|
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	49 cut -f 2- \|
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	50 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	51 #end for
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	52 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	53
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	54 sort -u regions_all.bed > regions_uniq.bed &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	55 ## split into even small chunks, this has some disatvantages and will not be used for the moment
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	56 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	57
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	58 mkdir vcf_output failed_alleles trace &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	59
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	60 ## Finished setting up inputs
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	61
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	62 for i in `cat regions_uniq.bed \| awk '{print $1":"$2".."$3}'`;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	63 do
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	64 echo "
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	65
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	66 ## COMMAND LINE STARTS HERE
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	67
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	68 freebayes
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	69
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	70 --region '\$i'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	71
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	72 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	73 --bam 'b_${bam_count}.bam'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	74 #end for
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	75 --fasta-reference '${reference_fasta_filename}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	76
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	77 ## Outputs
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	78 --vcf './vcf_output/part_\$i.vcf'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	79
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	80 ## Coverage
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	81 #if str($coverage_options.coverage_options_selector) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	82 @COVERAGE@
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	83 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	84
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	85 ##advanced options
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	86 #if str( $options_type.options_type_selector ) == "simple":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	87 #pass
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	88 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	89 --standard-filters
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	90 #elif str( $options_type.options_type_selector ) == "naive":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	91 --haplotype-length 0
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	92 --min-alternate-count 1
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	93 --min-alternate-fraction 0.05
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	94 --pooled-continuous
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	95 --report-monomorphic
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	96 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	97 --haplotype-length 0
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	98 --min-alternate-count 1
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	99 --min-alternate-fraction 0.05
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	100 --pooled-continuous
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	101 --report-monomorphic
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	102 --standard-filters
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	103 #elif str( $options_type.options_type_selector ) == "full":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	104 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	105 ${options_type.optional_inputs.report_monomorphic}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	106
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	107 #if $options_type.optional_inputs.output_trace_option:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	108 --trace ./trace/part_'\$i'.txt
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	109 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	110 #if $options_type.optional_inputs.output_failed_alleles_option:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	111 --failed-alleles ./failed_alleles/part_'\$i'.bed
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	112 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	113 #if $options_type.optional_inputs.samples:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	114 --samples '${options_type.optional_inputs.samples}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	115 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	116 #if $options_type.optional_inputs.populations:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	117 --populations '${options_type.optional_inputs.populations}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	118 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	119 #if $options_type.optional_inputs.A:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	120 --cnv-map '${options_type.optional_inputs.A}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	121 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	122 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	123 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	124 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	125 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	126 #if $options_type.optional_inputs.haplotype_basis_alleles:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	127 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	128 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	129 #if $options_type.optional_inputs.observation_bias:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	130 --observation-bias '${options_type.optional_inputs.observation_bias}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	131 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	132 #if $options_type.optional_inputs.contamination_estimates:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	133 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	134 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	135 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	136
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	137 ## REPORTING
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	138 #if str( $options_type.reporting.reporting_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	139 --pvar ${options_type.reporting.pvar}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	140 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	141 ## POPULATION MODEL
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	142 #if str( $options_type.population_model.population_model_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	143 --theta ${options_type.population_model.T}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	144 --ploidy ${options_type.population_model.P}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	145 ${options_type.population_model.J}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	146 ${options_type.population_model.K}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	147 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	148
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	149 ## REFERENCE ALLELE
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	150 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	151 ${options_type.reference_allele.Z}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	152 --reference-quality '${options_type.reference_allele.reference_quality}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	153 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	154
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	155 ## ALLELE SCOPE
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	156 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	157 ${options_type.allele_scope.I}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	158 ${options_type.allele_scope.i}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	159 ${options_type.allele_scope.X}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	160 ${options_type.allele_scope.u}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	161 ${options_type.allele_scope.no_partial_observations}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	162
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	163 -n ${options_type.allele_scope.n}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	164
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	165 --haplotype-length ${options_type.allele_scope.haplotype_length}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	166 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	167 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	168 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	169
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	170 ## REALIGNMENT
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	171 ${options_type.O}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	172
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	173 ##INPUT FILTERS
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	174 #if str( $options_type.input_filters.input_filters_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	175 ${options_type.input_filters.use_duplicate_reads}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	176 -m ${options_type.input_filters.m}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	177 -q ${options_type.input_filters.q}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	178 -R ${options_type.input_filters.R}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	179 -Y ${options_type.input_filters.Y}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	180 -e ${options_type.input_filters.e}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	181 -F ${options_type.input_filters.F}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	182 -C ${options_type.input_filters.C}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	183 -G ${options_type.input_filters.G}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	184
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	185 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	186 -Q ${options_type.input_filters.mismatch_filters.Q}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	187 #if str($options_type.input_filters.mismatch_filters.U)
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	188 -U ${options_type.input_filters.mismatch_filters.U}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	189 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	190 -z ${options_type.input_filters.mismatch_filters.z}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	191
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	192 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	193 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	194
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	195 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	196 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	197
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	198 ## POPULATION AND MAPPABILITY PRIORS
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	199 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	200 ${options_type.population_mappability_priors.k}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	201 ${options_type.population_mappability_priors.w}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	202 ${options_type.population_mappability_priors.V}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	203 ${options_type.population_mappability_priors.a}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	204 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	205
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	206 ## GENOTYPE LIKELIHOODS
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	207 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	208 ${$options_type.genotype_likelihoods.experimental_gls}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	209
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	210 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	211 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	212 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	213
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	214 ## ALGORITHMIC FEATURES
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	215 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	216 -B '${options_type.algorithmic_features.B}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	217 -W '${options_type.algorithmic_features.W}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	218 -D '${options_type.algorithmic_features.D}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	219
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	220 #if str($options_type.algorithmic_features.genotype_variant_threshold)
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	221 -S ${options_type.algorithmic_features.genotype_variant_threshold}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	222 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	223
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	224 ${options_type.algorithmic_features.N}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	225 ${options_type.algorithmic_features.j}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	226 ${options_type.algorithmic_features.H}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	227 ${options_type.algorithmic_features.genotype_qualities}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	228 ${options_type.algorithmic_features.report_genotype_likelihood_max}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	229
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	230 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	231 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	232 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	233
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	234 ";
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	235 done > freebayes_commands.sh &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	236
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	237 cat freebayes_commands.sh \|
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	238 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	239
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	240 ## make VCF header
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	241 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	242
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	243 for i in `cat regions_uniq.bed \| awk '{print $1":"$2".."$3}'`;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	244 do
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	245 ## if this fails then it bails out the script
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	246 cat "./vcf_output/part_\$i.vcf" \| grep -v "^#" \|\| true
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	247 ;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	248 done \| sort -k1,1 -k2,2n -k5,5 -u \| cat header.txt - > '${output_vcf}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	249
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	250 #if str( $options_type.options_type_selector ) == "full":
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	251 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	252 #if $options_type.optional_inputs.output_failed_alleles_option:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	253 &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	254 for i in `cat regions.bed \| awk '{print $1":"$2".."$3}'`;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	255 do
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	256 cat "./failed_alleles/part_\$i.bed"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	257 ;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	258 done > '${output_failed_alleles_bed}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	259 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	260
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	261 #if $options_type.optional_inputs.output_trace_option:
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	262 &&
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	263 for i in `cat regions.bed \| awk '{print $1":"$2".."$3}'`;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	264 do
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	265 cat './trace/part_\$i.txt'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	266 ;
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	267 done > '${output_trace}'
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	268 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	269 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	270 #end if
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	271 ]]></command>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	272
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	273 <inputs>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	274 <conditional name="reference_source">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	275 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	276 <option value="cached">Locally cached</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	277 <option value="history">History</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	278 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	279 <when value="cached">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	280 <expand macro="input_bam">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	281 <expand macro="validation" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	282 </expand>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	283 <param name="ref_file" type="select" label="Using reference genome">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	284 <options from_data_table="fasta_indexes" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	285 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	286 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	287 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	288 <when value="history"> <!-- FIX ME!!!! -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	289 <expand macro="input_bam" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	290 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	291 help="You can upload a FASTA sequence to the history and use it as reference" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	292 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	293 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	294 <conditional name="target_limit_type">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	295 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	296 <option value="do_not_limit" selected="true">Do not limit</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	297 <option value="limit_by_target_file">Limit by target file</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	298 <option value="limit_by_region">Limit to region</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	299 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	300 <when value="do_not_limit" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	301 <when value="limit_by_target_file">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	302 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	303 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	304 <when value="limit_by_region">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	305 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	306 <param name="region_start" type="integer" label="Region Start" value="" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	307 <param name="region_end" type="integer" label="Region End" value="" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	308 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	309 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	310 <conditional name="coverage_options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	311 <param name="coverage_options_selector" type="select" label="Read coverage"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	312 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	313 <option value="do_not_set" selected="true">Use defaults</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	314 <option value="set">Specify coverage options</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	315 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	316 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	317 <expand macro="par_min_cov" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	318 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	319 <when value="do_not_set" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	320 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	321 <conditional name="options_type">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	322 <param name="options_type_selector" type="select" label="Choose parameter selection level"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	323 help="Select how much control over the freebayes run you need">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	324 <option value="simple" selected="true">1. Simple diploid calling</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	325 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	326 <option value="naive">3. Frequency-based pooled calling</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	327 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	328 <option value="full">5. Full list of options</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	329 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	330 <when value="full">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	331
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	332 <conditional name="optional_inputs">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	333 <param name="optional_inputs_selector" type="select" label="Additional inputs"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	334 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	335 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	336 <option value="set">Provide additional inputs</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	337 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	338 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	339 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	340 label="Write out failed alleles file" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	341 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	342 label="Write out algorithm trace file" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	343 <param argument="--samples" type="data" format="txt"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	344 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	345 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	346 <param argument="--populations" type="data" format="txt" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	347 label="Populations dataset"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	348 help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	349 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	350 label="Read a copy number map from a BED dataset"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	351 help="The BED dataset should have the format: 'reference sequence, start, end, sample name, copy number' for each region in each sample which does not have the default copy number as set by --ploidy. If not specified, copy number is set to as specified by --ploidy" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	352 <conditional name="input_variant_type">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	353 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	354 <option value="do_not_provide" selected="true">Do not provide</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	355 <option value="provide_vcf">Provide VCF dataset</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	356 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	357 <when value="do_not_provide" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	358 <when value="provide_vcf">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	359 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	360 label="Use variants reported in this VCF dataset as input to the algorithm">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	361 <conversion name="Tabixized_input" type="tabix" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	362 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	363 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	364 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	365 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	366 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	367 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	368 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	369 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	370 label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	371 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	372 label="Load read length-dependent allele observation biases from"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	373 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	374 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	375 label="Upload per-sample estimates of contamination from"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	376 help="The format should be: sample p(read=R\|genotype=AR) p(read=A\|genotype=AA) Sample '*' can be used to set default contamination estimates" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	377 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	378 <when value="do_not_set" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	379 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	380
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	381 <!-- reporting -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	382 <conditional name="reporting">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	383 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	384 <option value="do_not_set" selected="true">Use defaults</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	385 <option value="set">Set reporting options</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	386 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	387 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	388 <param argument="--pvar" type="float" value="0.0"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	389 label="Report sites if the probability that there is a polymorphism at the site is greater than"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	390 help="Note that post-filtering is generally recommended over the use of this parameter" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	391 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	392 <when value="do_not_set" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	393 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	394
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	395 <!-- population model -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	396 <conditional name="population_model">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	397 <param name="population_model_selector" type="select" label="Population model options"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	398 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	399 <option value="do_not_set" selected="true">Use defaults</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	400 <option value="set">Set population model options</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	401 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	402 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	403 <param name="T" argument="--theta" type="float" value="0.001"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	404 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	405 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	406 <param name="P" argument="--ploidy" type="integer" value="2"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	407 label="Set ploidy for the analysis" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	408 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	409 label="Assume that samples result from pooled sequencing"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	410 help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	411 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	412 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	413 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	414 <when value="do_not_set" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	415 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	416
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	417 <!-- reference allele -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	418 <conditional name="reference_allele">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	419 <param name="reference_allele_selector" type="select" label="Reference allele options"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	420 help="Sets --use-reference-allele and --reference-quality options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	421 <option value="do_not_set" selected="true">Use defaults</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	422 <option value="set">Set reference allele options</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	423 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	424 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	425 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	426 label="Include the reference allele in the analysis as if it is another sample from the same population" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	427 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	428 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	429 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	430 <when value="do_not_set" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	431 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	432
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	433 <!-- allelic scope -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	434 <conditional name="allele_scope">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	435 <param name="allele_scope_selector" type="select" label="Allelic scope options"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	436 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	437 <option value="do_not_set" selected="true">Use defaults</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	438 <option value="set">Set alleic scope options</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	439 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	440 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	441 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	442 label="Ignore SNP alleles" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	443 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	444 label="Ignore indels alleles" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	445 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	446 label="Ignore multi-nucleotide polymorphisms, MNPs" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	447 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	448 label="Ignore complex events (composites of other classes)" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	449 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	450 label="How many best SNP alleles to evaluate"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	451 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	452 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	453 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	454 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	455 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	456 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	457 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	458 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	459 label="Exclude observations which do not fully span the dynamically-determined detection window"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	460 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	461 </when>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	462 <when value="do_not_set" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	463 </conditional>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	464
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	465 <!-- indel realignment -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	466 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	467 label="Turn off left-alignment of indels" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	468
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	469 <!-- input filters -->
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	470 <conditional name="input_filters">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	471 <param name="input_filters_selector" type="select" label="Input filters"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	472 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -$, -e, -0, -F, -C, -3, -G, and -! options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	473 <option value="do_not_set" selected="true">No input filters (default)</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	474 <option value="set">Set input filters</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	475 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	476 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	477 <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	478 label="Include duplicate-marked alignments in the analysis" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	479 <param name="m" argument="--min-mapping-quality" type="integer" value="1"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	480 label="Exclude alignments from analysis if they have a mapping quality less than" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	481 <param name="q" argument="--min-base-quality" type="integer" value="0"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	482 label="Exclude alleles from analysis if their supporting base quality less than" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	483 <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	484 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	485 <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	486 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	487 <conditional name="mismatch_filters">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	488 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	489 help="Sets -Q, -U, -z, and $ options">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	490 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	491 <option value="set">Set mismatch filters</option>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	492 </param>
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	493 <when value="set">
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	494 <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	495 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	496 <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	497 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	498 help="default=~unbounded" />
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	499 <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1" recetox parents: diff changeset	500 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />

0

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1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">

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2 <description>bayesian genetic variant detector</description>

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3 <macros>

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4 <import>macros.xml</import>

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5 </macros>

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6 <expand macro="requirements">

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7 <requirement type="package" version="4.1.3">gawk</requirement>

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8 <requirement type="package" version="20170422">parallel</requirement>

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9 </expand>

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10 <command detect_errors="exit_code"><![CDATA[

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11 ##set up input files

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12

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13 #set $reference_fasta_filename = "localref.fa"

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14

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15 #if str( $reference_source.reference_source_selector ) == "history":

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16 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&

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17 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&

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18 #else:

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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )

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20 #end if

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21

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22 #if $reference_source.batchmode.processmode == 'merge':

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23 #set $input_bamfiles = $reference_source.batchmode.input_bams

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24 #else:

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25 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]

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26 #end if

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27

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28 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):

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29 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&

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30 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&

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31 #end for

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32

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33 ## Tabixize optional input_variant_vcf file (for --variant-input option)

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34 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":

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35 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&

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36 ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&

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37 #end if

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38

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39 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions

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40 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":

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41 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&

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42 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":

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43 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&

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44 #else

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45 ##divide up the regions in the bam file for efficient processing

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46 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):

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47 samtools view -H b_${bam_count}.bam |

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48 grep '^@SQ' |

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49 cut -f 2- |

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50 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&

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51 #end for

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52 #end if

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53

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54 sort -u regions_all.bed > regions_uniq.bed &&

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55 ## split into even small chunks, this has some disatvantages and will not be used for the moment

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56 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&

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57

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58 mkdir vcf_output failed_alleles trace &&

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59

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60 ## Finished setting up inputs

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61

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62 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;

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63 do

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64 echo "

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65

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66 ## COMMAND LINE STARTS HERE

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67

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68 freebayes

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69

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70 --region '\$i'

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71

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72 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):

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73 --bam 'b_${bam_count}.bam'

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74 #end for

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75 --fasta-reference '${reference_fasta_filename}'

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76

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77 ## Outputs

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78 --vcf './vcf_output/part_\$i.vcf'

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79

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80 ## Coverage

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81 #if str($coverage_options.coverage_options_selector) == "set":

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82 @COVERAGE@

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83 #end if

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84

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85 ##advanced options

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86 #if str( $options_type.options_type_selector ) == "simple":

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87 #pass

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88 #elif str( $options_type.options_type_selector ) == "simple_w_filters":

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89 --standard-filters

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90 #elif str( $options_type.options_type_selector ) == "naive":

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91 --haplotype-length 0

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92 --min-alternate-count 1

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93 --min-alternate-fraction 0.05

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94 --pooled-continuous

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95 --report-monomorphic

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96 #elif str( $options_type.options_type_selector ) == "naive_w_filters":

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97 --haplotype-length 0

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98 --min-alternate-count 1

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99 --min-alternate-fraction 0.05

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100 --pooled-continuous

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101 --report-monomorphic

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102 --standard-filters

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103 #elif str( $options_type.options_type_selector ) == "full":

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104 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':

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105 ${options_type.optional_inputs.report_monomorphic}

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106

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107 #if $options_type.optional_inputs.output_trace_option:

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108 --trace ./trace/part_'\$i'.txt

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109 #end if

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110 #if $options_type.optional_inputs.output_failed_alleles_option:

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111 --failed-alleles ./failed_alleles/part_'\$i'.bed

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112 #end if

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113 #if $options_type.optional_inputs.samples:

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114 --samples '${options_type.optional_inputs.samples}'

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115 #end if

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116 #if $options_type.optional_inputs.populations:

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117 --populations '${options_type.optional_inputs.populations}'

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118 #end if

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119 #if $options_type.optional_inputs.A:

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120 --cnv-map '${options_type.optional_inputs.A}'

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121 #end if

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122 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":

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123 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above

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124 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}

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125 #end if

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126 #if $options_type.optional_inputs.haplotype_basis_alleles:

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127 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'

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128 #end if

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129 #if $options_type.optional_inputs.observation_bias:

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130 --observation-bias '${options_type.optional_inputs.observation_bias}'

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131 #end if

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132 #if $options_type.optional_inputs.contamination_estimates:

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133 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'

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134 #end if

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135 #end if

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136

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137 ## REPORTING

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138 #if str( $options_type.reporting.reporting_selector ) == "set":

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139 --pvar ${options_type.reporting.pvar}

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140 #end if

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141 ## POPULATION MODEL

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142 #if str( $options_type.population_model.population_model_selector ) == "set":

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143 --theta ${options_type.population_model.T}

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144 --ploidy ${options_type.population_model.P}

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145 ${options_type.population_model.J}

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146 ${options_type.population_model.K}

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147 #end if

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148

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149 ## REFERENCE ALLELE

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150 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":

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151 ${options_type.reference_allele.Z}

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152 --reference-quality '${options_type.reference_allele.reference_quality}'

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153 #end if

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154

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155 ## ALLELE SCOPE

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156 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":

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157 ${options_type.allele_scope.I}

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158 ${options_type.allele_scope.i}

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159 ${options_type.allele_scope.X}

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160 ${options_type.allele_scope.u}

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161 ${options_type.allele_scope.no_partial_observations}

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162

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163 -n ${options_type.allele_scope.n}

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164

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165 --haplotype-length ${options_type.allele_scope.haplotype_length}

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166 --min-repeat-size ${options_type.allele_scope.min_repeat_length}

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167 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}

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168 #end if

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169

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170 ## REALIGNMENT

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171 ${options_type.O}

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172

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173 ##INPUT FILTERS

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174 #if str( $options_type.input_filters.input_filters_selector ) == "set":

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175 ${options_type.input_filters.use_duplicate_reads}

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176 -m ${options_type.input_filters.m}

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177 -q ${options_type.input_filters.q}

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178 -R ${options_type.input_filters.R}

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179 -Y ${options_type.input_filters.Y}

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180 -e ${options_type.input_filters.e}

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181 -F ${options_type.input_filters.F}

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182 -C ${options_type.input_filters.C}

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183 -G ${options_type.input_filters.G}

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184

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185 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":

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186 -Q ${options_type.input_filters.mismatch_filters.Q}

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187 #if str($options_type.input_filters.mismatch_filters.U)

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188 -U ${options_type.input_filters.mismatch_filters.U}

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189 #end if

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190 -z ${options_type.input_filters.mismatch_filters.z}

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191

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192 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}

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193 #end if

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194

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195 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}

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196 #end if

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197

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198 ## POPULATION AND MAPPABILITY PRIORS

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199 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":

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200 ${options_type.population_mappability_priors.k}

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201 ${options_type.population_mappability_priors.w}

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202 ${options_type.population_mappability_priors.V}

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203 ${options_type.population_mappability_priors.a}

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204 #end if

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205

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206 ## GENOTYPE LIKELIHOODS

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207 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":

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208 ${$options_type.genotype_likelihoods.experimental_gls}

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209

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210 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}

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211 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}

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212 #end if

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213

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214 ## ALGORITHMIC FEATURES

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215 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":

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216 -B '${options_type.algorithmic_features.B}'

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217 -W '${options_type.algorithmic_features.W}'

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218 -D '${options_type.algorithmic_features.D}'

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219

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220 #if str($options_type.algorithmic_features.genotype_variant_threshold)

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221 -S ${options_type.algorithmic_features.genotype_variant_threshold}

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222 #end if

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223

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224 ${options_type.algorithmic_features.N}

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225 ${options_type.algorithmic_features.j}

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226 ${options_type.algorithmic_features.H}

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227 ${options_type.algorithmic_features.genotype_qualities}

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228 ${options_type.algorithmic_features.report_genotype_likelihood_max}

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229

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230 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}

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231 #end if

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232 #end if

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233

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234 ";

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235 done > freebayes_commands.sh &&

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236

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237 cat freebayes_commands.sh |

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238 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&

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239

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240 ## make VCF header

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241 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&

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242

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243 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;

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244 do

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245 ## if this fails then it bails out the script

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246 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true

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247 ;

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248 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'

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249

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250 #if str( $options_type.options_type_selector ) == "full":

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251 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':

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252 #if $options_type.optional_inputs.output_failed_alleles_option:

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253 &&

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254 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;

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255 do

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256 cat "./failed_alleles/part_\$i.bed"

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257 ;

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258 done > '${output_failed_alleles_bed}'

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259 #end if

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260

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261 #if $options_type.optional_inputs.output_trace_option:

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262 &&

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263 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;

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264 do

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265 cat './trace/part_\$i.txt'

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266 ;

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267 done > '${output_trace}'

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268 #end if

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269 #end if

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270 #end if

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271 ]]></command>

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272

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273 <inputs>

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274 <conditional name="reference_source">

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275 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">

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276 <option value="cached">Locally cached</option>

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277 <option value="history">History</option>

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278 </param>

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279 <when value="cached">

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280 <expand macro="input_bam">

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281 <expand macro="validation" />

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282 </expand>

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283 <param name="ref_file" type="select" label="Using reference genome">

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284 <options from_data_table="fasta_indexes" />

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285 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>

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286 </param>

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287 </when>

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288 <when value="history">

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289 <expand macro="input_bam" />

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290 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"

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291 help="You can upload a FASTA sequence to the history and use it as reference" />

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292 </when>

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293 </conditional>

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294 <conditional name="target_limit_type">

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295 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">

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296 <option value="do_not_limit" selected="true">Do not limit</option>

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297 <option value="limit_by_target_file">Limit by target file</option>

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298 <option value="limit_by_region">Limit to region</option>

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299 </param>

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300 <when value="do_not_limit" />

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301 <when value="limit_by_target_file">

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302 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />

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303 </when>

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304 <when value="limit_by_region">

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305 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" />

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306 <param name="region_start" type="integer" label="Region Start" value="" />

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307 <param name="region_end" type="integer" label="Region End" value="" />

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308 </when>

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309 </conditional>

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310 <conditional name="coverage_options">

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311 <param name="coverage_options_selector" type="select" label="Read coverage"

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312 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">

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313 <option value="do_not_set" selected="true">Use defaults</option>

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314 <option value="set">Specify coverage options</option>

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315 </param>

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316 <when value="set">

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317 <expand macro="par_min_cov" />

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318 </when>

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319 <when value="do_not_set" />

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320 </conditional>

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321 <conditional name="options_type">

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322 <param name="options_type_selector" type="select" label="Choose parameter selection level"

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323 help="Select how much control over the freebayes run you need">

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324 <option value="simple" selected="true">1. Simple diploid calling</option>

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325 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>

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326 <option value="naive">3. Frequency-based pooled calling</option>

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327 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>

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328 <option value="full">5. Full list of options</option>

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329 </param>

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330 <when value="full">

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331

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332 <conditional name="optional_inputs">

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333 <param name="optional_inputs_selector" type="select" label="Additional inputs"

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334 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">

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335 <option value="do_not_set" selected="true">Do not provide additional inputs</option>

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336 <option value="set">Provide additional inputs</option>

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337 </param>

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338 <when value="set">

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339 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"

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340 label="Write out failed alleles file" />

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341 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"

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342 label="Write out algorithm trace file" />

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343 <param argument="--samples" type="data" format="txt"

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344 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"

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345 help="By default FreeBayes will analyze all samples in its input BAM datasets" />

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346 <param argument="--populations" type="data" format="txt" optional="true"

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347 label="Populations dataset"

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348 help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />

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349 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"

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350 label="Read a copy number map from a BED dataset"

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351 help="The BED dataset should have the format: 'reference sequence, start, end, sample name, copy number' for each region in each sample which does not have the default copy number as set by --ploidy. If not specified, copy number is set to as specified by --ploidy" />

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352 <conditional name="input_variant_type">

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353 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">

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354 <option value="do_not_provide" selected="true">Do not provide</option>

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355 <option value="provide_vcf">Provide VCF dataset</option>

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356 </param>

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357 <when value="do_not_provide" />

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358 <when value="provide_vcf">

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359 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"

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diff changeset

360 label="Use variants reported in this VCF dataset as input to the algorithm">

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361 <conversion name="Tabixized_input" type="tabix" />

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362 </param>

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363 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"

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364 label="Only provide variant calls and genotype likelihoods for sites in VCF" />

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365 </when>

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366 </conditional>

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367 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"

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368 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />

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369 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"

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370 label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes" />

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371 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"

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372 label="Load read length-dependent allele observation biases from"

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373 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />

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374 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"

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375 label="Upload per-sample estimates of contamination from"

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376 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" />

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377 </when>

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378 <when value="do_not_set" />

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379 </conditional>

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380

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381

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382 <conditional name="reporting">

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383 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">

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384 <option value="do_not_set" selected="true">Use defaults</option>

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385 <option value="set">Set reporting options</option>

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386 </param>

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387 <when value="set">

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388 <param argument="--pvar" type="float" value="0.0"

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diff changeset

389 label="Report sites if the probability that there is a polymorphism at the site is greater than"

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parents:

diff changeset

390 help="Note that post-filtering is generally recommended over the use of this parameter" />

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parents:

diff changeset

391 </when>

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parents:

diff changeset

392 <when value="do_not_set" />

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parents:

diff changeset

393 </conditional>

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parents:

diff changeset

394

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parents:

diff changeset

395

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parents:

diff changeset

396 <conditional name="population_model">

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parents:

diff changeset

397 <param name="population_model_selector" type="select" label="Population model options"

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parents:

diff changeset

398 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

399 <option value="do_not_set" selected="true">Use defaults</option>

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parents:

diff changeset

400 <option value="set">Set population model options</option>

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parents:

diff changeset

401 </param>

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parents:

diff changeset

402 <when value="set">

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parents:

diff changeset

403 <param name="T" argument="--theta" type="float" value="0.001"

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

404 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

405 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />

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parents:

diff changeset

406 <param name="P" argument="--ploidy" type="integer" value="2"

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parents:

diff changeset

407 label="Set ploidy for the analysis" />

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parents:

diff changeset

408 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"

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parents:

diff changeset

409 label="Assume that samples result from pooled sequencing"

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

410 help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy" />

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parents:

diff changeset

411 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"

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parents:

diff changeset

412 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />

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parents:

diff changeset

413 </when>

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parents:

diff changeset

414 <when value="do_not_set" />

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parents:

diff changeset

415 </conditional>

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parents:

diff changeset

416

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

417

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

418 <conditional name="reference_allele">

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parents:

diff changeset

419 <param name="reference_allele_selector" type="select" label="Reference allele options"

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parents:

diff changeset

420 help="Sets --use-reference-allele and --reference-quality options">

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

421 <option value="do_not_set" selected="true">Use defaults</option>

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parents:

diff changeset

422 <option value="set">Set reference allele options</option>

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parents:

diff changeset

423 </param>

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parents:

diff changeset

424 <when value="set">

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parents:

diff changeset

425 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"

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parents:

diff changeset

426 label="Include the reference allele in the analysis as if it is another sample from the same population" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

427 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

428 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />

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parents:

diff changeset

429 </when>

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parents:

diff changeset

430 <when value="do_not_set" />

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parents:

diff changeset

431 </conditional>

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parents:

diff changeset

432

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

433

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parents:

diff changeset

434 <conditional name="allele_scope">

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parents:

diff changeset

435 <param name="allele_scope_selector" type="select" label="Allelic scope options"

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parents:

diff changeset

436 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

437 <option value="do_not_set" selected="true">Use defaults</option>

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parents:

diff changeset

438 <option value="set">Set alleic scope options</option>

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parents:

diff changeset

439 </param>

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parents:

diff changeset

440 <when value="set">

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parents:

diff changeset

441 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"

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parents:

diff changeset

442 label="Ignore SNP alleles" />

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parents:

diff changeset

443 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"

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parents:

diff changeset

444 label="Ignore indels alleles" />

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parents:

diff changeset

445 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"

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parents:

diff changeset

446 label="Ignore multi-nucleotide polymorphisms, MNPs" />

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parents:

diff changeset

447 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"

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parents:

diff changeset

448 label="Ignore complex events (composites of other classes)" />

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parents:

diff changeset

449 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"

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parents:

diff changeset

450 label="How many best SNP alleles to evaluate"

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

451 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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diff changeset

452 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

453 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

454 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"

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parents:

diff changeset

455 label="When assembling observations across repeats, require the total repeat length at least this many bp" />

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parents:

diff changeset

456 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"

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parents:

diff changeset

457 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

458 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"

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parents:

diff changeset

459 label="Exclude observations which do not fully span the dynamically-determined detection window"

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parents:

diff changeset

460 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

461 </when>

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parents:

diff changeset

462 <when value="do_not_set" />

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parents:

diff changeset

463 </conditional>

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parents:

diff changeset

464

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

465

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

466 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"

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parents:

diff changeset

467 label="Turn off left-alignment of indels" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

468

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

469

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

470 <conditional name="input_filters">

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parents:

diff changeset

471 <param name="input_filters_selector" type="select" label="Input filters"

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parents:

diff changeset

472 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -$, -e, -0, -F, -C, -3, -G, and -! options">

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

473 <option value="do_not_set" selected="true">No input filters (default)</option>

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diff changeset

474 <option value="set">Set input filters</option>

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diff changeset

475 </param>

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diff changeset

476 <when value="set">

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diff changeset

477 <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"

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diff changeset

478 label="Include duplicate-marked alignments in the analysis" />

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diff changeset

479 <param name="m" argument="--min-mapping-quality" type="integer" value="1"

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diff changeset

480 label="Exclude alignments from analysis if they have a mapping quality less than" />

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diff changeset

481 <param name="q" argument="--min-base-quality" type="integer" value="0"

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diff changeset

482 label="Exclude alleles from analysis if their supporting base quality less than" />

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diff changeset

483 <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0"

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diff changeset

484 label="Consider any allele in which the sum of qualities of supporting observations is at least" />

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diff changeset

485 <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0"

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diff changeset

486 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />

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diff changeset

487 <conditional name="mismatch_filters">

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488 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"

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diff changeset

489 help="Sets -Q, -U, -z, and $ options">

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diff changeset

490 <option value="do_not_set" selected="true">No mismatch filters (default)</option>

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491 <option value="set">Set mismatch filters</option>

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diff changeset

492 </param>

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diff changeset

493 <when value="set">

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diff changeset

494 <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10"

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diff changeset

495 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />

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diff changeset

496 <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true"

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diff changeset

497 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"

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diff changeset

498 help="default=~unbounded" />

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diff changeset

499 <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"

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diff changeset

500 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />

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diff changeset

501 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"

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diff changeset

502 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"

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diff changeset

503 help="default=~unbounded" />

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diff changeset

504 </when>

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diff changeset

505 <when value="do_not_set" />

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diff changeset

506 </conditional>

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diff changeset

507 <param name="e" argument="--read-indel-limit" type="integer" value="1000"

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parents:

diff changeset

508 label="Exclude reads with more than this number of separate gaps"

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diff changeset

509 help="default=~unbounded" />

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diff changeset

510 <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"

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diff changeset

511 label="Use stringent input base and mapping quality filters"

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diff changeset

512 help="Equivalent to -m 30 -q 20 -R 0 -S 0" />

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diff changeset

513 <param name="F" argument="--min-alternate-fraction" type="float" value="0.05"

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diff changeset

514 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />

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515 <param name="C" argument="--min-alternate-count" type="integer" value="2"

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diff changeset

516 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />

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diff changeset

517 <param name="min_alternate_qsum" argument="--min-alternate-qsum" type="integer" value="0"

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diff changeset

518 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />

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diff changeset

519 <param name="G" argument="--min-alternate-total" type="integer" value="1"

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diff changeset

520 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />

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diff changeset

521 </when>

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diff changeset

522 <when value="do_not_set" />

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diff changeset

523 </conditional>

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diff changeset

524

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diff changeset

525

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diff changeset

526 <conditional name="population_mappability_priors">

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diff changeset

527 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"

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diff changeset

528 help="Sets -k, -w, -V, and -a options">

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diff changeset

529 <option value="do_not_set" selected="true">Use defaults</option>

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diff changeset

530 <option value="set">Set population and mappability priors</option>

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diff changeset

531 </param>

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532 <when value="set">

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diff changeset

533 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"

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diff changeset

534 label="No population priors"

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diff changeset

535 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />

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diff changeset

536 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"

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diff changeset

537 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />

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538 <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"

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diff changeset

539 label="Disable incorporation of prior expectations about observations"

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diff changeset

540 help="Uses read placement probability, strand balance probability, and read position (5''-3'') probability" />

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541 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"

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diff changeset

542 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />

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diff changeset

543 </when>

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diff changeset

544 <when value="do_not_set" />

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diff changeset

545 </conditional>

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546

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547

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diff changeset

548 <conditional name="genotype_likelihoods">

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diff changeset

549 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"

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diff changeset

550 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">

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diff changeset

551 <option value="do_not_set" selected="true">Use defaults</option>

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552 <option value="set">Set genotype likelihood options</option>

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553 </param>

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diff changeset

554 <when value="set">

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diff changeset

555 <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"

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556 label="Limit estimated observation quality by capping base quality at" />

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557 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"

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558 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"

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559 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />

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560 <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"

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561 label="An estimate of contamination to use for all samples" />

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562 </when>

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563 <when value="do_not_set" />

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564 </conditional>

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565

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566

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567 <conditional name="algorithmic_features">

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568 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"

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569 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">

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570 <option value="do_not_set" selected="true">Use defaults</option>

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571 <option value="set">Set algorithmic features</option>

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572 </param>

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573 <when value="set">

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574 <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"

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575 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />

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576 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"

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577 label="Iterate no more than N times during genotyping step" />

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578 <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"

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579 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />

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580 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"

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581 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />

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582 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"

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583 label="Skip sample genotypings for which the sample has no supporting reads" />

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584 <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"

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585 label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample"

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586 help="default=~unbounded" />

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587 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"

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588 label="Use mapping quality of alleles when calculating data likelihoods" />

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589 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"

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590 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"

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591 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />

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592 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"

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593 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />

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594 <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"

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595 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />

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596 </when>

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597 <when value="do_not_set" />

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598 </conditional>

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599 </when>

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600 <when value="simple" />

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601 <when value="simple_w_filters" />

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602 <when value="naive" />

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603 <when value="naive_w_filters" />

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604 </conditional>

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605 </inputs>

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606 <outputs>

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607 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />

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608 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">

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609 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>

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610 </data>

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611 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">

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612 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>

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613 </data>

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614 </outputs>

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615 <tests>

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616 <test>

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617 <param name="reference_source_selector" value="history" />

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618 <param name="processmode" value="individual" />

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619 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>

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620 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>

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621 <param name="options_type_selector" value="simple"/>

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622 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />

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623 </test>

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624 <test>

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625 <param name="reference_source_selector" value="history" />

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626 <param name="processmode" value="individual" />

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627 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>

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628 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>

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629 <param name="options_type_selector" value="naive_w_filters"/>

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630 <param name="coverage_options_selector" value="set" />

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631 <param name="min_coverage" value="14"/>

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632 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />

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633 </test>

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634 <test>

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635 <param name="reference_source_selector" value="history" />

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636 <param name="processmode" value="individual" />

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637 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>

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638 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>

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639 <param name="options_type_selector" value="naive_w_filters"/>

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640 <param name="coverage_options_selector" value="set" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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641 <param name="min_coverage" value="14"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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642 <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />

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diff changeset

643 </test>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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644 <test>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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645 <param name="reference_source_selector" value="history" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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646 <param name="processmode" value="individual" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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647 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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648 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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649 <param name="options_type_selector" value="full"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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650 <param name="population_model_selector" value="set"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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651 <param name="P" value="1"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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diff changeset

652 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />

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653 </test>

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654 <test>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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655 <param name="reference_source_selector" value="history" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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656 <param name="processmode" value="individual" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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657 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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658 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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659 <param name="options_type_selector" value="simple"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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660 <param name="coverage_options_selector" value="set" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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661 <param name="min_coverage" value="250" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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662 <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />

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663 </test>

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664 <test>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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665 <param name="reference_source_selector" value="history" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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666 <param name="processmode" value="individual" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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667 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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668 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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669 <param name="options_type_selector" value="simple"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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670 <param name="coverage_options_selector" value="set" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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671 <param name="limit_coverage" value="400" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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672 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />

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673 </test>

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674 <test>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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675 <param name="reference_source_selector" value="history" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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676 <param name="processmode" value="individual" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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677 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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678 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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679 <param name="options_type_selector" value="simple"/>

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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680 <param name="coverage_options_selector" value="set" />

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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681 <param name="skip_coverage" value="100" />

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682 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />

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683 </test>

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684 </tests>

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685 <help><![CDATA[

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686 **What it does**

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687

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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688 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

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689

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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690 See https://github.com/ekg/freebayes for details on FreeBayes.

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691

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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692 ------

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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693

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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694 **Description**

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695

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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696 Provided some BAM dataset(s) and a reference sequence, FreeBayes will produce a VCF dataset describing SNPs, indels, and complex variants in samples in the input alignments.

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697

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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698 By default, FreeBayes will consider variants supported by at least 2 observations in a single sample (-C) and also by at least 20% of the reads from a single sample (-F). These settings are suitable to low to high depth sequencing in haploid and diploid samples, but users working with polyploid or pooled samples may wish to adjust them depending on the characteristics of their sequencing data.

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699

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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700 FreeBayes is capable of calling variant haplotypes shorter than a read length where multiple polymorphisms segregate on the same read. The maximum distance between polymorphisms phased in this way is determined by the --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be set to half the read length.

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701

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702 Ploidy may be set to any level (-p), but by default all samples are assumed to be diploid. FreeBayes can model per-sample and per-region variation in copy-number (-A) using a copy-number variation map.

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703

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704 FreeBayes can act as a frequency-based pooled caller and describe variants and haplotypes in terms of observation frequency rather than called genotypes. To do so, use --pooled-continuous and set input filters to a suitable level. Allele observation counts will be described by AO and RO fields in the VCF output.

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705

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706 -------

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707

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708 **Galaxy-specific options**

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709

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710 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:

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711

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712 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.

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713 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-variant-threshold 0) and --min-coverage.

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714 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling variants in mixtures such as viral, bacterial, or organellar genomes.

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715 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.

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716 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.

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717

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718 ------

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diff changeset

719

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

720 **Command-line parameters**

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

721

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

722 **Input**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

723

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

724 --bam FILE The file or set of BAM files to be analyzed.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

725 --bam-list FILE A file containing a list of BAM files to be analyzed.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

726

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

727 --stdin Read BAM input on stdin.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

728 --fasta-reference FILE Use FILE as the reference sequence for analysis.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

729 An index file (FILE.fai) will be created if none exists.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

730 If neither --targets nor --region are specified, FreeBayes

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

731 will analyze every position in this reference.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

732 --targets FILE Limit analysis to targets listed in the BED-format FILE.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

733 --region <chrom>:<start>-<end> Limit analysis to the specified region, 0-base coordinates,

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

734 end_position not included (same as BED format).

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

735 Either '-' or '..' maybe used as a separator.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

736 --samples FILE Limit analysis to samples listed (one per line) in the FILE.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

737 By default FreeBayes will analyze all samples in its input

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

738 BAM files.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

739 --populations FILE Each line of FILE should list a sample and a population which

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

740 it is part of. The population-based bayesian inference model

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

741 will then be partitioned on the basis of the populations.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

742 --cnv-map FILE Read a copy number map from the BED file FILE, which has

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

743 either a sample-level ploidy:

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

744 sample_name copy_number

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

745 or a region-specific format:

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

746 seq_name start end sample_name copy_number

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

747 ... for each region in each sample which does not have the

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

748 default copy number as set by --ploidy. These fields can be delimited

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

749 by space or tab.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

750

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

751 **Output**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

752

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

753 --vcf FILE Output VCF-format results to FILE. (default: stdout)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

754 --gvcf Write gVCF output, which indicates coverage in uncalled regions.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

755 --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

756 --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

757 set to "true" , will also route an int to --gvcf-chunk

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

758 similar to --output-mode EMIT_ALL_SITES from GATK

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

759 --variant-input VCF Use variants reported in VCF file as input to the algorithm.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

760 Variants in this file will included in the output even if

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

761 there is not enough support in the data to pass input filters.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

762 --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

763 and alleles which are provided in the VCF input, and provide

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

764 output in the VCF for all input alleles, not just those which

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

765 have support in the data.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

766 --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

767 VCF will be used for the construction of complex or haplotype

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

768 alleles.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

769 --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

770 provide information about all alleles in output, not only

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

771 those which are called.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

772 --report-monomorphic Report even loci which appear to be monomorphic, and report all

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

773 considered alleles, even those which are not in called genotypes.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

774 Loci which do not have any potential alternates have '.' for ALT.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

775 --pvar N Report sites if the probability that there is a polymorphism

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

776 at the site is greater than N. default: 0.0. Note that post-

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

777 filtering is generally recommended over the use of this parameter.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

778 --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

779

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

780 **Population model**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

781

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

782 --theta N The expected mutation rate or pairwise nucleotide diversity

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

783 among the population under analysis. This serves as the

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

784 single parameter to the Ewens Sampling Formula prior model

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

785 default: 0.001

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

786 --ploidy N Sets the default ploidy for the analysis to N. default: 2

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

787 --pooled-discrete Assume that samples result from pooled sequencing.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

788 Model pooled samples using discrete genotypes across pools.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

789 When using this flag, set --ploidy to the number of

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

790 alleles in each sample or use the --cnv-map to define

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

recetox

parents:

diff changeset

791 per-sample ploidy.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

792 --pooled-continuous Output all alleles which pass input filters, regardles of

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

793 genotyping outcome or model.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

794

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

795 **Reference allele**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

796

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

797 --use-reference-allele This flag includes the reference allele in the analysis as

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

798 if it is another sample from the same population.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

799 --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

800 site and base quality of BQ. default: 100,60

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

801

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

802 **Allele scope**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

803

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

804 --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

805 supporting quality scores. (Set to 0 to use all; default: all)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

806 --max-complex-gap

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

807 --haplotype-length N Allow haplotype calls with contiguous embedded matches of up

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

808 to this length. Set N=-1 to disable clumping. (default: 3)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

809 --min-repeat-size When assembling observations across repeats, require the total repeat

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

810 length at least this many bp. (default: 5)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

811 --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

812 entropy > N bits per bp. Set to 0 to turn off. (default: 1)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

813 --no-partial-observations Exclude observations which do not fully span the dynamically-determined

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

814 detection window. (default, use all observations, dividing partial

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

815 support across matching haplotypes when generating haplotypes.)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

816

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

817 **Indel realignment**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

818

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

819 --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

820

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

821 **Input filters**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

822

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

823 --use-duplicate-reads Include duplicate-marked alignments in the analysis.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

824 default: exclude duplicates marked as such in alignments

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

825 --min-mapping-quality Q Exclude alignments from analysis if they have a mapping

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

826 quality less than Q. default: 1

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

827 --min-base-quality Q Exclude alleles from analysis if their supporting base

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

828 quality is less than Q. default: 0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

829 --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

830 observations is at least Q. default: 0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

831 --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

832 supporting reads is at least Q. default: 0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

833 --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

834 quality of the mismatch is >= Q. default: 10

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

835 --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

836 has base quality >= mismatch-base-quality-threshold.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

837 default: ~unbounded

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

838 --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

839 each mismatch has base quality >= mismatch-base-quality-threshold

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

840 default: 1.0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

841 --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

842 with quality >= mismatch-base-quality-threshold.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

843 default: ~unbounded

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

844 --read-indel-limit N Exclude reads with more than N separate gaps.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

845 default: ~unbounded

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

846 --standard-filters Use stringent input base and mapping quality filters

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

847 Equivalent to -m 30 -q 20 -R 0 -S 0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

848 --min-alternate-fraction N Require at least this fraction of observations supporting

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

849 an alternate allele within a single individual in the

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

850 in order to evaluate the position. default: 0.05

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

851 --min-alternate-count N Require at least this count of observations supporting

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

852 an alternate allele within a single individual in order

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

853 to evaluate the position. default: 2

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

854 --min-alternate-qsum N Require at least this sum of quality of observations supporting

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

855 an alternate allele within a single individual in order

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

856 to evaluate the position. default: 0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

857 --min-alternate-total N Require at least this count of observations supporting

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

858 an alternate allele within the total population in order

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

859 to use the allele in analysis. default: 1

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

860 --min-coverage N Require at least this coverage to process a site. default: 0

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

861 --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

862 default: no limit

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

863 --skip-coverage N Skip processing of alignments overlapping positions with coverage >N.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

864 This filters sites above this coverage, but will also reduce data nearby.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

865 default: no limit

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

866

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

867 **Population priors**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

868

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

869 --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

870 Ewens Sampling Formula component of priors.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

871

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

872 **Mappability priors**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

873

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

874 --hwe-priors-off Disable estimation of the probability of the combination

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

875 arising under HWE given the allele frequency as estimated

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

876 by observation frequency.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

877 --binomial-obs-priors-off Disable incorporation of prior expectations about observations.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

878 Uses read placement probability, strand balance probability,

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

879 and read position (5'-3') probability.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

880 --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

881 as a component of the priors.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

882

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

883 **Genotype likelihoods**::

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

884

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

885 --observation-bias FILE Read length-dependent allele observation biases from FILE.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

886 The format is [length] [alignment efficiency relative to reference]

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

887 where the efficiency is 1 if there is no relative observation bias.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

888 --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

889 --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

890 --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

891 --contamination-estimates FILE A file containing per-sample estimates of contamination, such as

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

892 those generated by VerifyBamID. The format should be:

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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parents:

diff changeset

893 sample p(read=R|genotype=AR) p(read=A|genotype=AA)

13bde05924da "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 4b9af142d00f49fdc99bc635ec5ca1db032b1fc1"

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894 Sample '*' can be used to set default contamination estimates.

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895

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896 **Algorithmic features**::

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897

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898 --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided

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899 from genotype likelihoods.

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900 --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.

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901 --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when

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902 genotyping. default: 6.

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903 --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space

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904 which include no more than N samples with their Mth best

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905 data likelihood. default: 1,3.

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906 --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.

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907 --genotype-variant-threshold N Limit posterior integration to samples where the second-best

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908 genotype likelihood is no more than log(N) from the highest

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909 genotype likelihood for the sample. default: ~unbounded

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910 --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.

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911 --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the

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912 distance from the indel. By default use a minimum BQ in flanking sequence.

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913 --read-dependence-factor N Incorporate non-independence of reads by scaling successive

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914 observations by this factor during data likelihood

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915 calculations. default: 0.9

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916 --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in

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917 each sample field in the VCF output.

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918

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919 ------

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920

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921 **Acknowledgments**

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922

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923 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.

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924 TNG was developed by Bjoern Gruening.

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925 ]]>

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926 </help>

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927 <expand macro="citations">

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928 <citation type="bibtex">

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929 @article{Tange2011a,

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930 title = {GNU Parallel - The Command-Line Power Tool},

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931 author = {O. Tange},

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932 address = {Frederiksberg, Denmark},

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933 journal = {;login: The USENIX Magazine},

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934 month = {Feb},

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935 number = {1},

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936 volume = {36},

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937 url = {http://www.gnu.org/s/parallel},

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938 year = {2011},

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939 pages = {42-47}

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940 }

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941 </citation>

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942 </expand>

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943 </tool>

Mercurial > repos > recetox > freebayes

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